Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023207.1 Corchorus olitorius cultivar O-4 contig23240, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 25480
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:847 original size:28 final size:28
Alignment explanation
Indices: 812--971 Score: 216
Period size: 28 Copynumber: 5.7 Consensus size: 28
802 TAGCCTAGCG
* *
812 AAATGACCAAAATGCCCCTAGATGTACA
1 AAATGACCAAAATGCCCCTGGATGTGCA
* * * *
840 AAACGACCAAACTGCCCTTGGATGTTCAA
1 AAATGACCAAAATGCCCCTGGATGTGC-A
869 AAATGACCAAAATGCCCCTGGA--TGCA
1 AAATGACCAAAATGCCCCTGGATGTGCA
895 AAAGTGACCAAAATGCCCCCTGGATGTGCA
1 AAA-TGACCAAAATG-CCCCTGGATGTGCA
925 AAATGACCAAAATGCCCCTGGATGTGCA
1 AAATGACCAAAATGCCCCTGGATGTGCA
*
953 AAACGACCAAAATGCCCCT
1 AAATGACCAAAATGCCCCT
972 CCTTAGGTGA
Statistics
Matches: 117, Mismatches: 10, Indels: 10
0.85 0.07 0.07
Matches are distributed among these distances:
26 4 0.03
27 13 0.11
28 62 0.53
29 31 0.26
30 7 0.06
ACGTcount: A:0.38, C:0.28, G:0.18, T:0.17
Consensus pattern (28 bp):
AAATGACCAAAATGCCCCTGGATGTGCA
Found at i:971 original size:56 final size:57
Alignment explanation
Indices: 812--971 Score: 227
Period size: 57 Copynumber: 2.8 Consensus size: 57
802 TAGCCTAGCG
* * * * *
812 AAATGACCAAAATGCCCCTAGATGTACAAAACGACCAAACTGCCCTTGGATGTTCAA
1 AAATGACCAAAATGCCCCTGGATGTGCAAAACGACCAAAATGCCCCTGGATGTGCAA
*
869 AAATGACCAAAATGCCCCTGGA--TGCAAAAGTGACCAAAATGCCCCCTGGATGTGC-A
1 AAATGACCAAAATGCCCCTGGATGTGCAAAA-CGACCAAAATG-CCCCTGGATGTGCAA
925 AAATGACCAAAATGCCCCTGGATGTGCAAAACGACCAAAATGCCCCT
1 AAATGACCAAAATGCCCCTGGATGTGCAAAACGACCAAAATGCCCCT
972 CCTTAGGTGA
Statistics
Matches: 92, Mismatches: 7, Indels: 9
0.85 0.06 0.08
Matches are distributed among these distances:
55 6 0.07
56 37 0.40
57 42 0.46
58 7 0.08
ACGTcount: A:0.38, C:0.28, G:0.18, T:0.17
Consensus pattern (57 bp):
AAATGACCAAAATGCCCCTGGATGTGCAAAACGACCAAAATGCCCCTGGATGTGCAA
Found at i:5051 original size:16 final size:17
Alignment explanation
Indices: 5019--5051 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5009 TTATCCTATC
5019 TTAGTTTAGATTATTAT
1 TTAGTTTAGATTATTAT
*
5036 TTAGTTTGGA-TATTAT
1 TTAGTTTAGATTATTAT
5052 AAGGGTTGAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (17 bp):
TTAGTTTAGATTATTAT
Found at i:5948 original size:16 final size:17
Alignment explanation
Indices: 5916--5948 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5906 TTATCCTATC
5916 TTAGTTTAGATTATTAT
1 TTAGTTTAGATTATTAT
*
5933 TTAGTTTGGA-TATTAT
1 TTAGTTTAGATTATTAT
5949 AAGGGTTGGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (17 bp):
TTAGTTTAGATTATTAT
Found at i:6015 original size:897 final size:897
Alignment explanation
Indices: 4280--6075 Score: 3403
Period size: 897 Copynumber: 2.0 Consensus size: 897
4270 TCACTGCACA
4280 CTAAGTAGATGTATTAGCTAATATACTTGGGTTTATTTTGTTATCATTAAAAACAATAGGGTTCA
1 CTAAGTAGATGTATTAGCTAATATACTTGGGTTTATTTTGTTATCATTAAAAACAATAGGGTTCA
* * *
4345 ACACCAGGGGAATTTTCAAGGAAGGCCAATGAATTTTCAAAGGCCTAATTTTCAACAATCTTTAC
66 ACACCAAGGAAATTTTCAAGGAAGGCCAATGAATATTCAAAGGCCTAATTTTCAACAATCTTTAC
4410 AAGTTTCCATCGAGATGCAACAAATAAGAGAAGCTATGAAGATGATGAGGAAACAAATTAGTCAA
131 AAGTTTCCATCGAGATGCAACAAATAAGAGAAGCTATGAAGATGATGAGGAAACAAATTAGTCAA
4475 CTGGCTAATGACATGAGTGAGCTCAAGACACAAGGTCAACAAAGGATCCCATCACAACCAAAGGT
196 CTGGCTAATGACATGAGTGAGCTCAAGACACAAGGTCAACAAAGGATCCCATCACAACCAAAGGT
4540 GCCTCCTAGGGAGAATATAAGTGCAATTACTTTGAGAAGTGGAAAAGAGTTTAAAGAACCCTATC
261 GCCTCCTAGGGAGAATATAAGTGCAATTACTTTGAGAAGTGGAAAAGAGTTTAAAGAACCCTATC
*
4605 CAATCCATGTCGTACAAGATGAAGGAGAGCCGAGTTTAATGCGCCCAAGAATGATCATGATCATG
326 CAACCCATGTCGTACAAGATGAAGGAGAGCCGAGTTTAATGCGCCCAAGAATGATCATGATCATG
*
4670 GAGAGCATGGAGAGGATGCACAAGGGCTGCATGGAAGCGTGAAGATGCAAGGAGACAATGGAGAT
391 GAGAACATGGAGAGGATGCACAAGGGCTGCATGGAAGCGTGAAGATGCAAGGAGACAATGGAGAT
4735 ATCGATGGGATTGTTTCAAGACCAAAGAAGATGCCATTTGATCCTTTGAGCTTGCCTGAAGGTCC
456 ATCGATGGGATTGTTTCAAGACCAAAGAAGATGCCATTTGATCCTTTGAGCTTGCCTGAAGGTCC
*
4800 AATGACAAGATCAAGAGCCAAAAAGTTCAAGGATACACTCATGGGCATTATTCGAACTCATCTTG
521 AATGACAAGATCAAGAACCAAAAAGTTCAAGGATACACTCATGGGCATTATTCGAACTCATCTTG
4865 AAGATATGAAGTCCATCGAAGTGCAATTGAAGAGCTTTGGAGTTGATTTGAGCAAGAAGGCACCC
586 AAGATATGAAGTCCATCGAAGTGCAATTGAAGAGCTTTGGAGTTGATTTGAGCAAGAAGGCACCC
* **
4930 ATCGGTTCCAAGTTCATCACTTTACTTGCTATTAATGCTTAAATGGGCATGTAAAGACCCACTCG
651 ATCGGTTCCAAGTTCATCACTTTACTTACTATTAATGCTTAAATGAACATGTAAAGACCCACTCG
4995 TCCATACGAGGCCTTTATCCTATCTTAGTTTAGATTATTATTTAGTTTGGATATTATAAGGGTTG
716 TCCATACGAGGCCTTTATCCTATCTTAGTTTAGATTATTATTTAGTTTGGATATTATAAGGGTTG
5060 AGCCTTGTTTAATTAAATTCCAATCGTTGTTTGAGTCTGTTTTTATTATTTATTTTCCTAGTTGG
781 AGCCTTGTTTAATTAAATTCCAATCGTTGTTTGAGTCTGTTTTTATTATTTATTTTCCTAGTTGG
5125 ACTTGAACTAGTTTTCCTTATCCTTATTTAAGCCCAAACCGCCCCATAAGGG
846 ACTTGAACTAGTTTTCCTTATCCTTATTTAAGCCCAAACCGCCCCATAAGGG
5177 CTAAGTAGATGTATTAGCTAATATACTTGGGTTTATTTTGTTATCATTAAAAACAATAGGGTTCA
1 CTAAGTAGATGTATTAGCTAATATACTTGGGTTTATTTTGTTATCATTAAAAACAATAGGGTTCA
5242 ACACCAAGGAAATTTTCAAGGAAGGCCAATGAATATTCAAAGGCCTAATTTTCAACAATCTTTAC
66 ACACCAAGGAAATTTTCAAGGAAGGCCAATGAATATTCAAAGGCCTAATTTTCAACAATCTTTAC
* * *
5307 AAGTTTCCATCGAGATGCAACAAATAAGAGAAGTTATGGAGATGATGAGGAAACAAATTAGTCCA
131 AAGTTTCCATCGAGATGCAACAAATAAGAGAAGCTATGAAGATGATGAGGAAACAAATTAGTCAA
5372 CTGGCTAATGACATGAGTGAGCTCAAGACACAAGGTCAACAAAGGATCCCATCACAACCAAAGGT
196 CTGGCTAATGACATGAGTGAGCTCAAGACACAAGGTCAACAAAGGATCCCATCACAACCAAAGGT
5437 GCCTCCTAGGGAGAATATAAGTGCAATTACTTTGAGAAGTGGAAAAGAGTTTAAAGAACCCTATC
261 GCCTCCTAGGGAGAATATAAGTGCAATTACTTTGAGAAGTGGAAAAGAGTTTAAAGAACCCTATC
**
5502 CAACCCATGTCGTACAAGATGAAGGAGAGCCGAGTTTAATGCGCCCAAGGCTGATCATGATCATG
326 CAACCCATGTCGTACAAGATGAAGGAGAGCCGAGTTTAATGCGCCCAAGAATGATCATGATCATG
5567 GAGAACATGGAGAGGATGCACAAGGGCTGCATGGAAGCGTGAAGATGCAAGGAGACAATGGAGAT
391 GAGAACATGGAGAGGATGCACAAGGGCTGCATGGAAGCGTGAAGATGCAAGGAGACAATGGAGAT
5632 ATCGATGGGATTGTTTCAAGACCAAAGAAGATGCCATTTGATCCTTTGAGCTTGCCTGAAGGTCC
456 ATCGATGGGATTGTTTCAAGACCAAAGAAGATGCCATTTGATCCTTTGAGCTTGCCTGAAGGTCC
5697 AATGACAAGATCAAGAACCAAAAAGTTCAAGGATACACTCATGGGCATTATTCGAACTCATCTTG
521 AATGACAAGATCAAGAACCAAAAAGTTCAAGGATACACTCATGGGCATTATTCGAACTCATCTTG
5762 AAGATATGAAGTCCATCGAAGTGCAATTGAAGAGCTTTGGAGTTGATTTGAGCAAGAAGGCACCC
586 AAGATATGAAGTCCATCGAAGTGCAATTGAAGAGCTTTGGAGTTGATTTGAGCAAGAAGGCACCC
* *
5827 ATCGGTTCCAAGTTCATCACTTTGCTTACTATTAATGCTTAAATGAACATGTAAAGACCCACTTG
651 ATCGGTTCCAAGTTCATCACTTTACTTACTATTAATGCTTAAATGAACATGTAAAGACCCACTCG
5892 TCCATACGAGGCCTTTATCCTATCTTAGTTTAGATTATTATTTAGTTTGGATATTATAAGGGTTG
716 TCCATACGAGGCCTTTATCCTATCTTAGTTTAGATTATTATTTAGTTTGGATATTATAAGGGTTG
* * *
5957 GGCCTTGTTTAATTAAATTCCAATCGTTGTTTGAGTGTGTTTTTATTATTTATTTTCCTTGTTGG
781 AGCCTTGTTTAATTAAATTCCAATCGTTGTTTGAGTCTGTTTTTATTATTTATTTTCCTAGTTGG
* *
6022 ATTTGGACTAGTTTTCCTTATCCTTATTTAAGCCCAAACCGCCCCATAAGGG
846 ACTTGAACTAGTTTTCCTTATCCTTATTTAAGCCCAAACCGCCCCATAAGGG
6074 CT
1 CT
6076 TTATTTTCTT
Statistics
Matches: 878, Mismatches: 21, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
897 878 1.00
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.28
Consensus pattern (897 bp):
CTAAGTAGATGTATTAGCTAATATACTTGGGTTTATTTTGTTATCATTAAAAACAATAGGGTTCA
ACACCAAGGAAATTTTCAAGGAAGGCCAATGAATATTCAAAGGCCTAATTTTCAACAATCTTTAC
AAGTTTCCATCGAGATGCAACAAATAAGAGAAGCTATGAAGATGATGAGGAAACAAATTAGTCAA
CTGGCTAATGACATGAGTGAGCTCAAGACACAAGGTCAACAAAGGATCCCATCACAACCAAAGGT
GCCTCCTAGGGAGAATATAAGTGCAATTACTTTGAGAAGTGGAAAAGAGTTTAAAGAACCCTATC
CAACCCATGTCGTACAAGATGAAGGAGAGCCGAGTTTAATGCGCCCAAGAATGATCATGATCATG
GAGAACATGGAGAGGATGCACAAGGGCTGCATGGAAGCGTGAAGATGCAAGGAGACAATGGAGAT
ATCGATGGGATTGTTTCAAGACCAAAGAAGATGCCATTTGATCCTTTGAGCTTGCCTGAAGGTCC
AATGACAAGATCAAGAACCAAAAAGTTCAAGGATACACTCATGGGCATTATTCGAACTCATCTTG
AAGATATGAAGTCCATCGAAGTGCAATTGAAGAGCTTTGGAGTTGATTTGAGCAAGAAGGCACCC
ATCGGTTCCAAGTTCATCACTTTACTTACTATTAATGCTTAAATGAACATGTAAAGACCCACTCG
TCCATACGAGGCCTTTATCCTATCTTAGTTTAGATTATTATTTAGTTTGGATATTATAAGGGTTG
AGCCTTGTTTAATTAAATTCCAATCGTTGTTTGAGTCTGTTTTTATTATTTATTTTCCTAGTTGG
ACTTGAACTAGTTTTCCTTATCCTTATTTAAGCCCAAACCGCCCCATAAGGG
Found at i:8323 original size:16 final size:16
Alignment explanation
Indices: 8292--8345 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
8282 GCGGGTTTGA
*
8292 GTTCGGGTA-CTTCGG
1 GTTCGGGTATTTTCGG
8307 GTTCGGGTATTTTCGG
1 GTTCGGGTATTTTCGG
* *
8323 GCTCGGGT-TATGTCGG
1 GTTCGGGTAT-TTTCGG
8339 GTTCGGG
1 GTTCGGG
8346 CTCGGGTTTG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
15 10 0.30
16 23 0.70
ACGTcount: A:0.06, C:0.17, G:0.43, T:0.35
Consensus pattern (16 bp):
GTTCGGGTATTTTCGG
Found at i:8504 original size:13 final size:12
Alignment explanation
Indices: 8481--8527 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
8471 AAGTTTATTG
8481 ATAATATATAAT
1 ATAATATATAAT
8493 ATAATAATATAAT
1 ATAAT-ATATAAT
* *
8506 ATAACAT-TATT
1 ATAATATATAAT
8517 ATCAATATATA
1 AT-AATATATA
8528 TAAAGATTGA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
11 5 0.17
12 11 0.38
13 13 0.45
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.40
Consensus pattern (12 bp):
ATAATATATAAT
Found at i:8813 original size:31 final size:31
Alignment explanation
Indices: 8778--8849 Score: 78
Period size: 31 Copynumber: 2.3 Consensus size: 31
8768 TAAATTATTG
*
8778 CAAATTAAAACAAAT-TAAG-CATTAAATTAAA
1 CAAATTAAAA-AAATGAAAGTC-TTAAATTAAA
*
8809 CAAA-TAATTAAAATGAAAGTCTTAAATTAAA
1 CAAATTAA-AAAAATGAAAGTCTTAAATTAAA
8840 CAAATTAAAA
1 CAAATTAAAA
8850 GCTGATAGAC
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
30 7 0.21
31 23 0.68
32 4 0.12
ACGTcount: A:0.61, C:0.08, G:0.04, T:0.26
Consensus pattern (31 bp):
CAAATTAAAAAAATGAAAGTCTTAAATTAAA
Found at i:9090 original size:2 final size:2
Alignment explanation
Indices: 9085--9117 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
9075 TTATATAAGT
9085 TA TA TA TA TA T- TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
9118 GTAGTTTAGC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:9092 original size:11 final size:11
Alignment explanation
Indices: 9084--9116 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
9074 GTTATATAAG
9084 TTATATATATA
1 TTATATATATA
9095 TTATATATATA
1 TTATATATATA
9106 -TATATATATA
1 TTATATATATA
9116 T
1 T
9117 AGTAGTTTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.48
11 11 0.52
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
TTATATATATA
Found at i:9309 original size:16 final size:16
Alignment explanation
Indices: 9287--9332 Score: 74
Period size: 16 Copynumber: 2.9 Consensus size: 16
9277 AATTCAAATT
9287 ATTTCGGGTTCGGGTA
1 ATTTCGGGTTCGGGTA
* *
9303 TTTTCGGGCTCGGGTA
1 ATTTCGGGTTCGGGTA
9319 ATTTCGGGTTCGGG
1 ATTTCGGGTTCGGG
9333 ACGTTGACTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.09, C:0.15, G:0.39, T:0.37
Consensus pattern (16 bp):
ATTTCGGGTTCGGGTA
Found at i:14642 original size:39 final size:38
Alignment explanation
Indices: 14546--14648 Score: 113
Period size: 39 Copynumber: 2.7 Consensus size: 38
14536 AATATGATTC
14546 TGAAAT-TAACTGATAAGCAATGATCCTAAATCAGGAT
1 TGAAATATAACTGATAAGCAATGATCCTAAATCAGGAT
** * *
14583 CAAAATAAAACTGCCA-AAGCAAT-ATTCCTAAATCATGAT
1 TGAAATATAACTG--ATAAGCAATGA-TCCTAAATCAGGAT
14622 TGAAATATAACTGATGAAGCAATGATC
1 TGAAATATAACTGAT-AAGCAATGATC
14649 AAGACTCAAA
Statistics
Matches: 52, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
37 5 0.10
38 6 0.12
39 39 0.75
40 2 0.04
ACGTcount: A:0.46, C:0.16, G:0.14, T:0.25
Consensus pattern (38 bp):
TGAAATATAACTGATAAGCAATGATCCTAAATCAGGAT
Found at i:14774 original size:30 final size:30
Alignment explanation
Indices: 14740--15161 Score: 621
Period size: 30 Copynumber: 13.9 Consensus size: 30
14730 CTGTTGAAGT
*
14740 AATGATCCTTAACCAGGATTAAAATAAAGC
1 AATGATCCTAAACCAGGATTAAAATAAAGC
* *
14770 AATGATCCTCAACCAGGATTAAAATAAAGT
1 AATGATCCTAAACCAGGATTAAAATAAAGC
* *
14800 AATGATCCTCAACCAGAATTAAAATAAAGC
1 AATGATCCTAAACCAGGATTAAAATAAAGC
* *
14830 AATGATCCTAAACCAGGATTGAAATGAAGC
1 AATGATCCTAAACCAGGATTAAAATAAAGC
* * *
14860 AATAATCCTCAACCAGGATTAAAATAAAAC
1 AATGATCCTAAACCAGGATTAAAATAAAGC
* * *
14890 AATGATCCTAAAGCAGGATTAAGAGAAAGC
1 AATGATCCTAAACCAGGATTAAAATAAAGC
*
14920 AATGATCCTAAACCAGGACTAAAATGAAA-C
1 AATGATCCTAAACCAGGATTAAAAT-AAAGC
*
14950 AATGATCCTCAACCAGGATTAAAATAAAGC
1 AATGATCCTAAACCAGGATTAAAATAAAGC
14980 AATGATCCTAAACCAGGATTAAAAATAAAGC
1 AATGATCCTAAACCAGGATT-AAAATAAAGC
*
15011 AATGATCCTCAACCAGGATTAAAAATAAAGC
1 AATGATCCTAAACCAGGATT-AAAATAAAGC
15042 AATGATCCTAAACCAGGATTAAAATAAAGC
1 AATGATCCTAAACCAGGATTAAAATAAAGC
* *
15072 AATAATCCTAAACTAGGATTAAAAATAAAGC
1 AATGATCCTAAACCAGGATT-AAAATAAAGC
15103 AATGATCCTAAACCAGGATTAAAATAAAGC
1 AATGATCCTAAACCAGGATTAAAATAAAGC
*
15133 AATGATCCTAAACCAGGATCGAAAATAAA
1 AATGATCCTAAACCAGGAT-TAAAATAAA
15162 CTAATAAAAT
Statistics
Matches: 354, Mismatches: 33, Indels: 9
0.89 0.08 0.02
Matches are distributed among these distances:
29 3 0.01
30 253 0.71
31 98 0.28
ACGTcount: A:0.49, C:0.17, G:0.14, T:0.20
Consensus pattern (30 bp):
AATGATCCTAAACCAGGATTAAAATAAAGC
Found at i:15635 original size:71 final size:71
Alignment explanation
Indices: 15548--16417 Score: 894
Period size: 71 Copynumber: 12.3 Consensus size: 71
15538 CAATTTGCGG
* * * *
15548 TCAACTGAAATAAACTGAAGCAAGATCGCCTTGGATCAACTGAAATAGACTGTAGAAAAGATCGC
1 TCAACTGAAATAAACTGAAGAAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAAGATCGC
15613 CCTGGA
66 CCTGGA
* * * * * * *
15619 TCAACTGAAATGAACTGAAGAAAGACCACCCTGGGTCAACTGAAATGAATTGAAG-AAAGATCAC
1 TCAACTGAAATAAACTGAAGAAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAAGATCGC
*
15683 CCTGTA
66 CCTGGA
* * * * *
15689 TCAACTAAAATAAATTGAAGAAAGACCGCCCTGGGTCAACTGAAATAAACTGAAGAAAA-ATCAC
1 TCAACTGAAATAAACTGAAGAAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAAGATCGC
*
15753 CTTGGA
66 CCTGGA
* * * * *
15759 TCAACTGAAATAAATTGAAGAAAGATCACCCTGGATCGACTGAAATAAAATTGAAG-GAAGA-CA
1 TCAACTGAAATAAACTGAAGAAAGATCGCCCTGGATCAACTGAAAT-AAACTGAAGAAAAGATC-
*
15822 GCCCTGGG
64 GCCCTGGA
* * *
15830 TCAACTGAAATAAACTGAATAAAAGATCGCCCTGGATCAACTGAAATGAACTGAAGAAAAGATCA
1 TCAACTGAAATAAACTGAA-GAAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAAGATCG
*
15895 CCCTAGA
65 CCCTGGA
* * * ** * * *
15902 TCAACTAAAATAAACTAAATAAAAGATCGCCCTGGATCAACTGACGTAAATTG-AGGAGAGATCG
1 TCAACTGAAATAAACTGAA-GAAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAAGATCG
*
15966 TCCTGGA
65 CCCTGGA
* * * *
15973 TCAATTGAAATGAACTGAAGAAAAGATCGCCCTGGATTAACTGAAATAAACTAAATG-AAAGATC
1 TCAACTGAAATAAACTGAAG-AAAGATCGCCCTGGATCAACTGAAATAAACTGAA-GAAAAGATC
*
16037 ACCCTGGA
64 GCCCTGGA
* * * * * * * *
16045 TCAACTGAAGTAAATTGAGGAGAGATCACCCTGGATCAATTGAAATGAACTGAAGAAAGGATCGC
1 TCAACTGAAATAAACTGAAGAAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAAGATCGC
* *
16110 CTTAGA
66 CCTGGA
* * * * * * * *
16116 TCAACTAAAATAAACTAAATAAAATATCGCCCTGGATCAACTGAAGTAAATTG-AGGAGAGATCG
1 TCAACTGAAATAAACTGAA-GAAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAAGATCG
*
16180 TCCTGGA
65 CCCTGGA
* * * * *
16187 TCAATTGAAATGAACTGAAGAAAGATCACCCTGGATCAACTGAAATAAATTGAATAAAAGATCGC
1 TCAACTGAAATAAACTGAAGAAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAAGATCGC
16252 CCTGGA
66 CCTGGA
* * * * *
16258 TCAACTGAAGTAAATTG-AGTAAAGATCGCTCTGGATCAACTGAAATAAACTAAATAAAAGATCG
1 TCAACTGAAATAAACTGAAG-AAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAAGATCG
16322 CCCTGGA
65 CCCTGGA
* * * * * * *
16329 TCAACTTAAGTAAATTGAGGAAAGATCACCCTGGATCAATTGAAATGAACTGAAG-AAAGATCGC
1 TCAACTGAAATAAACTGAAGAAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAAGATCGC
16393 CCTGGA
66 CCTGGA
*
16399 TCAACTAAAATAAACTGAA
1 TCAACTGAAATAAACTGAA
16418 TACAGACCAC
Statistics
Matches: 654, Mismatches: 130, Indels: 31
0.80 0.16 0.04
Matches are distributed among these distances:
70 177 0.27
71 341 0.52
72 134 0.20
73 2 0.00
ACGTcount: A:0.43, C:0.18, G:0.19, T:0.20
Consensus pattern (71 bp):
TCAACTGAAATAAACTGAAGAAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAAGATCGC
CCTGGA
Found at i:15971 original size:107 final size:106
Alignment explanation
Indices: 15548--16431 Score: 912
Period size: 107 Copynumber: 8.3 Consensus size: 106
15538 CAATTTGCGG
* * * * * * *
15548 TCAACTGAAATAAACTGAAGCAAGATCGCCTTGGATCAACTGAAATAGACTGTAGAAAAGATCGC
1 TCAACTGAAATGAACTGAAGAAAGATCACCCTGGATCAACTGAAATAAACTGAATAAAAGATCGC
* * * * *
15613 CCTGGATCAACTGAAATGAACTGAAGAAAGACCACCCTGGG
66 CCTGGATCAACTGAAATAAACTGAGGAAAGATCGCCCTGGA
* * * * * *
15654 TCAACTGAAATGAATTGAAGAAAGATCACCCTGTATCAACTAAAATAAATTGAA-GAAAGACCGC
1 TCAACTGAAATGAACTGAAGAAAGATCACCCTGGATCAACTGAAATAAACTGAATAAAAGATCGC
* * * * *
15718 CCTGGGTCAACTGAAATAAACTGAAGAAAAATCACCTTGGA
66 CCTGGATCAACTGAAATAAACTGAGGAAAGATCGCCCTGGA
* * * * **
15759 TCAACTGAAATAAATTGAAGAAAGATCACCCTGGATCGACTGAAATAAAATTGAA-GGAAGA-CA
1 TCAACTGAAATGAACTGAAGAAAGATCACCCTGGATCAACTGAAAT-AAACTGAATAAAAGATC-
* **
15822 GCCCTGGGTCAACTGAAATAAACTGAATAAAAGATCGCCCTGGA
64 GCCCTGGATCAACTGAAATAAACTG-AGGAAAGATCGCCCTGGA
* * *
15866 TCAACTGAAATGAACTGAAGAAAAGATCACCCTAGATCAACTAAAATAAACTAAATAAAAGATCG
1 TCAACTGAAATGAACTGAAG-AAAGATCACCCTGGATCAACTGAAATAAACTGAATAAAAGATCG
** * * *
15931 CCCTGGATCAACTGACGTAAATTGAGGAGAGATCGTCCTGGA
65 CCCTGGATCAACTGAAATAAACTGAGGAAAGATCGCCCTGGA
* * * * * *
15973 TCAATTGAAATGAACTGAAGAAAAGATCGCCCTGGATTAACTGAAATAAACTAAATGAAAGATCA
1 TCAACTGAAATGAACTGAAG-AAAGATCACCCTGGATCAACTGAAATAAACTGAATAAAAGATCG
* * * *
16038 CCCTGGATCAACTGAAGTAAATTGAGGAGAGATCACCCTGGA
65 CCCTGGATCAACTGAAATAAACTGAGGAAAGATCGCCCTGGA
* * * * * * *
16080 TCAATTGAAATGAACTGAAGAAAGGATCGCCTTAGATCAACTAAAATAAACTAAATAAAATATCG
1 TCAACTGAAATGAACTGAAGAAA-GATCACCCTGGATCAACTGAAATAAACTGAATAAAAGATCG
* * * *
16145 CCCTGGATCAACTGAAGTAAATTGAGGAGAGATCGTCCTGGA
65 CCCTGGATCAACTGAAATAAACTGAGGAAAGATCGCCCTGGA
* *
16187 TCAATTGAAATGAACTGAAGAAAGATCACCCTGGATCAACTGAAATAAATTGAATAAAAGATCGC
1 TCAACTGAAATGAACTGAAGAAAGATCACCCTGGATCAACTGAAATAAACTGAATAAAAGATCGC
* * * *
16252 CCTGGATCAACTGAAGTAAATTGAGTAAAGATCGCTCTGGA
66 CCTGGATCAACTGAAATAAACTGAGGAAAGATCGCCCTGGA
* * * * * * * ** *
16293 TCAACTGAAATAAACTAAATAAAAGATCGCCCTGGATCAACTTAAGTAAATTG-AGGAAAGATCA
1 TCAACTGAAATGAACTGAA-GAAAGATCACCCTGGATCAACTGAAATAAACTGAATAAAAGATCG
* * *
16357 CCCTGGATCAATTGAAATGAACTGAAGAAAGATCGCCCTGGA
65 CCCTGGATCAACTGAAATAAACTGAGGAAAGATCGCCCTGGA
* * * * *
16399 TCAACTAAAATAAACTGAATACAGACCACCCTG
1 TCAACTGAAATGAACTGAAGAAAGATCACCCTG
16432 AGTCACTTGG
Statistics
Matches: 672, Mismatches: 98, Indels: 17
0.85 0.12 0.02
Matches are distributed among these distances:
105 96 0.14
106 233 0.35
107 294 0.44
108 48 0.07
109 1 0.00
ACGTcount: A:0.42, C:0.18, G:0.19, T:0.20
Consensus pattern (106 bp):
TCAACTGAAATGAACTGAAGAAAGATCACCCTGGATCAACTGAAATAAACTGAATAAAAGATCGC
CCTGGATCAACTGAAATAAACTGAGGAAAGATCGCCCTGGA
Found at i:16431 original size:35 final size:35
Alignment explanation
Indices: 15548--16417 Score: 898
Period size: 35 Copynumber: 24.5 Consensus size: 35
15538 CAATTTGCGG
* *
15548 TCAACTGAAATAAACTGAAGCAAGATCGCCTTGGA
1 TCAACTGAAATAAACTGAAGAAAGATCGCCCTGGA
* *
15583 TCAACTGAAATAGACTGTAGAAAAGATCGCCCTGGA
1 TCAACTGAAATAAACTGAAG-AAAGATCGCCCTGGA
* * * *
15619 TCAACTGAAATGAACTGAAGAAAGACCACCCTGGG
1 TCAACTGAAATAAACTGAAGAAAGATCGCCCTGGA
* * * *
15654 TCAACTGAAATGAATTGAAGAAAGATCACCCTGTA
1 TCAACTGAAATAAACTGAAGAAAGATCGCCCTGGA
* * * *
15689 TCAACTAAAATAAATTGAAGAAAGACCGCCCTGGG
1 TCAACTGAAATAAACTGAAGAAAGATCGCCCTGGA
* * *
15724 TCAACTGAAATAAACTGAAGAAAAATCACCTTGGA
1 TCAACTGAAATAAACTGAAGAAAGATCGCCCTGGA
* *
15759 TCAACTGAAATAAATTGAAGAAAGATCACCCTGGA
1 TCAACTGAAATAAACTGAAGAAAGATCGCCCTGGA
* * * *
15794 TCGACTGAAATAAAATTGAAGGAAGA-CAGCCCTGGG
1 TCAACTGAAAT-AAACTGAAGAAAGATC-GCCCTGGA
*
15830 TCAACTGAAATAAACTGAATAAAAGATCGCCCTGGA
1 TCAACTGAAATAAACTGAA-GAAAGATCGCCCTGGA
* * *
15866 TCAACTGAAATGAACTGAAGAAAAGATCACCCTAGA
1 TCAACTGAAATAAACTGAAG-AAAGATCGCCCTGGA
* * *
15902 TCAACTAAAATAAACTAAATAAAAGATCGCCCTGGA
1 TCAACTGAAATAAACTGAA-GAAAGATCGCCCTGGA
** * * * *
15938 TCAACTGACGTAAATTGAGGAGAGATCGTCCTGGA
1 TCAACTGAAATAAACTGAAGAAAGATCGCCCTGGA
* *
15973 TCAATTGAAATGAACTGAAGAAAAGATCGCCCTGGA
1 TCAACTGAAATAAACTGAAG-AAAGATCGCCCTGGA
* * *
16009 TTAACTGAAATAAACTAAATGAAAGATCACCCTGGA
1 TCAACTGAAATAAACTGAA-GAAAGATCGCCCTGGA
* * * * *
16045 TCAACTGAAGTAAATTGAGGAGAGATCACCCTGGA
1 TCAACTGAAATAAACTGAAGAAAGATCGCCCTGGA
* * * *
16080 TCAATTGAAATGAACTGAAGAAAGGATCGCCTTAGA
1 TCAACTGAAATAAACTGAAGAAA-GATCGCCCTGGA
* * * *
16116 TCAACTAAAATAAACTAAATAAAATATCGCCCTGGA
1 TCAACTGAAATAAACTGAA-GAAAGATCGCCCTGGA
* * * * *
16152 TCAACTGAAGTAAATTGAGGAGAGATCGTCCTGGA
1 TCAACTGAAATAAACTGAAGAAAGATCGCCCTGGA
* * *
16187 TCAATTGAAATGAACTGAAGAAAGATCACCCTGGA
1 TCAACTGAAATAAACTGAAGAAAGATCGCCCTGGA
* *
16222 TCAACTGAAATAAATTGAATAAAAGATCGCCCTGGA
1 TCAACTGAAATAAACTGAA-GAAAGATCGCCCTGGA
* * *
16258 TCAACTGAAGTAAATTG-AGTAAAGATCGCTCTGGA
1 TCAACTGAAATAAACTGAAG-AAAGATCGCCCTGGA
* *
16293 TCAACTGAAATAAACTAAATAAAAGATCGCCCTGGA
1 TCAACTGAAATAAACTGAA-GAAAGATCGCCCTGGA
* * * * *
16329 TCAACTTAAGTAAATTGAGGAAAGATCACCCTGGA
1 TCAACTGAAATAAACTGAAGAAAGATCGCCCTGGA
* *
16364 TCAATTGAAATGAACTGAAGAAAGATCGCCCTGGA
1 TCAACTGAAATAAACTGAAGAAAGATCGCCCTGGA
*
16399 TCAACTAAAATAAACTGAA
1 TCAACTGAAATAAACTGAA
16418 TACAGACCAC
Statistics
Matches: 679, Mismatches: 141, Indels: 30
0.80 0.17 0.04
Matches are distributed among these distances:
35 369 0.54
36 305 0.45
37 5 0.01
ACGTcount: A:0.43, C:0.18, G:0.19, T:0.20
Consensus pattern (35 bp):
TCAACTGAAATAAACTGAAGAAAGATCGCCCTGGA
Found at i:25090 original size:1 final size:1
Alignment explanation
Indices: 25084--25161 Score: 66
Period size: 1 Copynumber: 78.0 Consensus size: 1
25074 ATAAATATGC
* * * * * * * *
25084 AAAAAAAAAACAAAAAACAAAAAAAACACAAAAAAACAAAAAAAAAAACAAAAAACAAAAAAAGA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* *
25149 AACAAAAGAAAAA
1 AAAAAAAAAAAAA
25162 TTGAAAATTG
Statistics
Matches: 57, Mismatches: 20, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 57 1.00
ACGTcount: A:0.87, C:0.10, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:25106 original size:19 final size:19
Alignment explanation
Indices: 25084--25155 Score: 110
Period size: 19 Copynumber: 3.8 Consensus size: 19
25074 ATAAATATGC
25084 AAAAAAAAAACAAAAAAC-
1 AAAAAAAAAACAAAAAACA
*
25102 AAAAAAAACACAAAAAAACA
1 AAAAAAAAAAC-AAAAAACA
25122 AAAAAAAAAACAAAAAACA
1 AAAAAAAAAACAAAAAACA
*
25141 AAAAAAGAAACAAAA
1 AAAAAAAAAACAAAA
25156 GAAAAATTGA
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.20
19 29 0.59
20 10 0.20
ACGTcount: A:0.88, C:0.11, G:0.01, T:0.00
Consensus pattern (19 bp):
AAAAAAAAAACAAAAAACA
Found at i:25130 original size:31 final size:30
Alignment explanation
Indices: 25084--25161 Score: 97
Period size: 31 Copynumber: 2.6 Consensus size: 30
25074 ATAAATATGC
*
25084 AAAAAA-AAAACAAAAAACAAAAAA-AACACA
1 AAAAAACAAAAAAAAAAACAAAAAACAA-A-A
25114 AAAAAACAAAAAAAAAAACAAAAAACAAAA
1 AAAAAACAAAAAAAAAAACAAAAAACAAAA
*
25144 AAAGAAACAAAAGAAAAA
1 AAA-AAACAAAAAAAAAA
25162 TTGAAAATTG
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
30 10 0.23
31 31 0.72
32 2 0.05
ACGTcount: A:0.87, C:0.10, G:0.03, T:0.00
Consensus pattern (30 bp):
AAAAAACAAAAAAAAAAACAAAAAACAAAA
Done.